In this operation, the gang breaks up into three groups, with each assigned a job that must be done in order to stop Toothpick. Murray is the lone man as he must take the van back by destroying electrical barriers surrounding the van. He must use TNT on the train to blow them up, while dealing with rat troopers parachuting in. Once he does this, Murray drives the van off the back of the train and speeds up to catch the next group, Bentley and Carmelita. Bentley must get to a computer and hack the trains whistles in order to annoy Toothpick. Carmelita clears the way by shooting the steers guarding the computer, and then Bentley hacks it to gain access to the trains whistles. Then the 2 jump into the van and got to catch Sly and Tennessee. Tennessee is up first as he makes his way through the interior of the train to steal back the gold Toothpick stole from him. Kid is able to line Bentley up perfectly with the gold as he steals 3 carts worth of gold back. He is then captured by the rat troopers and Toothpick steals his gun. Sly then engages with Toothpick in a fianl showdown in an atttempt to get Kid's gun back.
The boss fight begins with Toothpick throwing out three balls that cover the floor in lasers. Switch to your jailbird costume and then use the Ball Roll move to roll over the balls, shutting off the lasers. Toothpick will begin to throw dynamite at you. The objective here is to use the jailbird costume's ball to push 3 large buttons. After throwing some dynamite, Toothpick will mount a turret and begin shooting at you. Once you have hit all 3 buttons, the train whistles will activate. This will cause Toothpick to grow large in a fit of rage. He will jump around the stage trying to squash you. Sprinting is especially useful in dodging him. He will eventually stop jumping around and will send a barrage of miniature whirlwinds at you. Jump over the smaller ones, and run away from the larger ones. After that, use you jailbird costume ball to knock Toothpick into the furnace, then run up to him and whack him with you cane until a third of his health is gone. After that, the process will start over. Complete this 2 more times to defeat Toothpick once and for all.
With Toothpick defeated, he is shot out of the furnace and lands right in front of Tennessee, who kicks him of the train. The raccoon then jumps off the train himself. As Sly is celebrating Toothpick's defeat, Bentley notices that the train is headed for a broken bridge. Sly jumps onto the van, and Murray tries to stop it. However, the brakes don't work, so the gang and the van drive off the cliff. In desperation, Bentley grabs Murray's fossil necklace and throws it into the time machine. The van time travels before it crashes to the ground, much to the gang's relief. However, they end up stuck in an unknown time period.
- In the cutscene after Bentley hacks the terminal, Toothpick's subtitles are erroneously green, Bentley's signature color, instead of yellow or brown, which Toothpick's subtitles are usually colored.